Sunday, 22 April 2007

Molecular graphics tutorial

So far you have drawn your structure and optimised it. The next step is making a nice looking graphic out of it.

The program that I like to use for this is PyMOL. It works great but I have to admit that I haven't tried any other comparable programs. First you open the molecule file that you just produced. On the right side its name appears. Go there and click zoom. Change the the preset to "ball and stick". Change the color to how you want your carbons and then go for color by element. The carbons will stay the way you had them.

I usually like a 1440x900 picture because that fits my screen. With typing "viewport 960,600" the window is on scale and I can still see everything. I rotate and zoom the molecule until it looks nice. Then I type "ray 1440,900" to raytrace the picture. If I like it I save it. If I don't I can change some of the settings.

PyMOL related links are: the official manual - it definitely makes sense to work through that once. PyMOL scripts - I use a modified pymolrc file to set the background color and the viewport. PyMOLWiki - I haven't really found much information I could use there.

POV-Ray is a raytracing program that can be used in connection with ArgusLab. ArgusLab has an option for exporting into the POV-Ray format. I don't think it is as convenient to use as PyMOL. I don't like the pictures as much either. It probably has much more options but PyMOL has a few very nice looking presets.

jmol offers a possibility for having interactive molecule models on web pages based on java. To use jmol you need a webspace where you put the files for running jmol and the molecule files. The applet appears if you add a few lines of javascript code to your webpage. For using jmol in blogspot I open the .js file in the header. Inside my post I have the following code (there are no line breaks because blogspot will add <br /> and create large spaces):

<div style="border: 1px solid grey;"><script type="text/javascript">jmolInitialize(" .../blog/jmol");jmolApplet(500, "load .../blog/molfiles/BINAP-PM3.mol;");</script></div>

The problem is that the browser crashes if two applets are opened like this on same page. Maybe the problem is that "jmolInitialize" is carried out twice. I might be able to solve the problem if I put that into the header, too. But I am not sure about that and who needs so many moving things anyway. I can't put an applet here for that reason but you can look at BINAP.


Tim said...

Great set of posts, thanks so much. Unfortunately, I'm not on windows so I've been working to track down corresponding software for either mac or linux. I tried TINKER, and also had minimal success - it's very finicky. Now I'm playing around with GAMESS and so far, so good.

Thanks again!

Felix said...

you're welcome. I haven't really figured out what to do with GAMESS. I know how I can run the test jobs. but I am looking for a way to look at the input and output files other than the text editor.

Tim said...

Try checking out Ghemical as a graphical frontend - you can build structures and submit them to GAMESS using a graphical queue called GTK-GAMESS. For backend stuff, MacMolPlt looks pretty nice so far - it can read GAMESS logs (among others) and nicely display orbitals/normal modes/etc.



Felix said...

thanks, I guess I should have read that first page of the introduction :) i just found that yesterday. right now I am using chemcraft which is nice for showing the results. I'll have to get ghemical

Anonymous said...

Chem3D can be used as a graphical interface for GAMESS. Or slightly less used friendly but free Winmostar

Felix said...

thanks, I'll give it a try if I have some time